Amino Acids
Learning the structure and function of the 20 amino acids is not difficult. It requires critical thinking, discovering patterns, and 1-2 hours. We will analyze each amino acid to learn its side chain, functional group type, 3 letter code, and 1 letter code.
Backbone for all amino acids (X= side chain): H3N-XCH-COO
1.Glycine:
X= H (Nonpolar)
Gly,G
Simplest amino acid so gets “first choice” of 3 letter and 1 letter code (there are other amino acids that start with G but they do not get G as their 1 letter code!)
2. Alanine:
X= CH3 (Nonpolar)
“All”anine= Glycine except with “All” the hydrogens and extra carbon! (CH3 instead of H!)
Ala,A
Second simplest amino acid so gets “first choice” of 3 letter and 1 letter code (there are other amino acids that start with A but they do not get A as their 1 letter code!)
3. Valine:
X= CH-(CH3)2 (Nonpolar)
The V in Valine looks like a peace sign! Valine is a girl with short fingers making a peace sign(CH joint with two CH3 fingers coming off)
Val, V
V and Val are the first portions of the name so amino acid so gets these as the 3 letter and 1 letter code.
4. Leucine:
X= CH2-CH-(CH3)2 (Nonpolar)
Leucine is like Valine except 1 carbon longer! Leucine is a taller boy with long fingers making a peace sign.
Leu, L
5.Isoleucine
X= HC(CH3)CH2CH3
Isoleucine has the same formula as leucine except instead of a peace sign it is a “middle finger” ie the longer chain is now in the middle (middle finger) and there is a short finger on the side.
6.Methionine:
X= CH2-CH2-S-CH3 (Nonpolar because sulfur is capped with CH3)
“Meth” “smells bad” so does sulfur. Methionine has 3 carbons and a sulfur which is capped with a CH3 thus preventing it from reacting or making the amino acid basic.
Met, M
7. Phenylalanine
X = CH2-BenzeneRing (Nonpolar because benzene ring is nonpolar)
Alanine with a benzene ring on it. Don’t forget the extra carbon!
Phe, F
The 1 letter code can be memorizing by thinking “Feenylalanine”
8. Tryptophan
X= 2 Huge Blocks with a nitrogen-containing pentagon and benzene
Trp, W
“Whiptophan” so W is 1 letter code. T,R, and P will be taken by other amino acids.
9. Serine
X= CH2OH (Polar because of OH)
Alcoholic version of alanine
Ser, S
10. Cysteine
X= CH2SH (Polar because of S)
Sulfur version of alanine
Cys, C (NOT S!)
11. Threonine
X=HO-HC-CH3 (Polar because of OH)
Like alcoholic valine except one of the CH3 is completely replaced with an OH
Thr, T
Simplest of all the amino acids that start with letter T so gets first choice to have T as 1 letter code!
12. Tyrosine
X= CH2BenzeneOH
Like Phenylalanine with an OH on it (Phe + Ser = Tyr)
Tyr, Y
Y is the second letter in tyrosine so it is used as 1 letter code becase T is already taken by threonine.
13. Proline
X= (Nitrogen on backbone)-CH2CH2CH2-(Central Carbon on backbone) (Polar because the N involved from backbone)
Proline is a pro at breaking protein structures because it causes a kink
Pro,P
14. Asparagine
X=CH2CONH2 (Polar because of NH2 and C=O)
Like aspartate except COO replaced with NH2
Asn, N
Asparagine is an assassiN taking the place of aspartate. Rather than Asp, we write asN because the N correlates to the N to signify the Nitrogen in the molecule. Since A and S are already taken, N is our 1 letter code.
15. Glutamine
X=CH2CH2CONH2 (Polar because of NH2 and C=O)
Like glutamate except COO replaced with NH2
Gln, Q
Glutamine is so Qute-amine! Q from qutamine is the 1 letter code since G, L, and N were already taking. We write Gln rather than Glu because Glu is for glutamate and the N in Gln helps signify the extra nitrogen in the amino acid.
16. Lysine
X= CH2CH2CH2CH2NH3 (basic because of nitrogen)
Lysss = sound of long slivering snake (long carbon tail)
Small NH3 cap
Lys, K
K= koaLa (L for lysine, L in KoaLa which started with K. L,Y, S 1 letter codes already taken.)
17. Arginine
X=CH2CH2CH2NHCNH2NH2 (basic because of nitrogen)
ARRRRginine is on a pirate’s ship with a complex docking bay surrounding the central carbon. The docking bay has 3 portals, like the 3 nitrogen coming off the tip of the chain.
Arg, R
R= aRRRRGinine
18. Histidine
X=CH2-RingW/2Nitrogens (basic because of nitrogen)
19. Aspartate/Aspartic Acid
X=CH2COO (acidic because of COO)
Asparagine w/out the NH2
Asp, D
asparDate D= 1 letter code
20. Glutamate/Glutamic Acid
X=CH2CH2COO (acidic because of COO)
Longer Aspartate
Glu, E
glutamatE E=1 letter code
Problem: Draw In The Side Chains and Label Each Amino Acid With The 3 and 1 Letter Code
